forked from pool/python-biopython
Matej Cepl
30a50e8f9e
- Update to version 1.7.8.
* The main change is that Bio.Alphabet is no longer used. In some
cases you will now have to specify expected letters, molecule
type (DNA, RNA, protein), or gap character explicitly.
* Bio.SeqIO.parse() is faster with "fastq" format due to small
improvements in the Bio.SeqIO.QualityIO module.
* The SeqFeature object's .extract() method can now be used for
trans-spliced locations via an optional dictionary of references.
* As in recent releases, more of our code is now explicitly
available under either our original "Biopython License Agreement",
or the very similar but more commonly used "3-Clause BSD License".
See the LICENSE.rst file for more details.
* Additionally, a number of small bugs and typos have been fixed
with additions to the test suite. There has been further work to
follow the Python PEP8, PEP257 and best practice standard coding
style, and all of the tests have been reformatted with the black
tool to match the main code base.
- Skip python36 because numpy no longer support it.
OBS-URL: https://build.opensuse.org/request/show/874100
OBS-URL: https://build.opensuse.org/package/show/devel:languages:python:numeric/python-biopython?expand=0&rev=13
85 lines
2.5 KiB
RPMSpec
85 lines
2.5 KiB
RPMSpec
#
|
|
# spec file for package python-biopython
|
|
#
|
|
# Copyright (c) 2021 SUSE LLC
|
|
#
|
|
# All modifications and additions to the file contributed by third parties
|
|
# remain the property of their copyright owners, unless otherwise agreed
|
|
# upon. The license for this file, and modifications and additions to the
|
|
# file, is the same license as for the pristine package itself (unless the
|
|
# license for the pristine package is not an Open Source License, in which
|
|
# case the license is the MIT License). An "Open Source License" is a
|
|
# license that conforms to the Open Source Definition (Version 1.9)
|
|
# published by the Open Source Initiative.
|
|
|
|
# Please submit bugfixes or comments via https://bugs.opensuse.org/
|
|
#
|
|
|
|
|
|
%{?!python_module:%define python_module() python-%{**} python3-%{**}}
|
|
# Tests require a network connection
|
|
%bcond_with test
|
|
%define skip_python2 1
|
|
%define skip_python36 1
|
|
Name: python-biopython
|
|
Version: 1.78
|
|
Release: 0
|
|
Summary: Python Tools for Computational Molecular Biology
|
|
License: MIT AND BSD-3-Clause
|
|
URL: http://www.biopython.org
|
|
Source0: https://files.pythonhosted.org/packages/source/b/biopython/biopython-%{version}.tar.gz
|
|
Source100: python-biopython-rpmlintrc
|
|
BuildRequires: %{python_module devel}
|
|
BuildRequires: %{python_module numpy-devel}
|
|
BuildRequires: %{python_module setuptools}
|
|
BuildRequires: %{python_module xml}
|
|
BuildRequires: fdupes
|
|
BuildRequires: flex
|
|
BuildRequires: python-rpm-macros
|
|
Requires: python-numpy
|
|
Requires: python-xml
|
|
Recommends: python-matplotlib
|
|
Recommends: python-mysql
|
|
Recommends: python-networkx
|
|
Recommends: python-psycopg2
|
|
Recommends: python-pydot
|
|
Recommends: python-pygraphviz
|
|
Recommends: python-rdflib
|
|
Recommends: python-reportlab
|
|
%python_subpackages
|
|
|
|
%description
|
|
The Biopython Project is an international association of developers of freely
|
|
available Python tools for computational molecular biology.
|
|
|
|
%prep
|
|
%setup -q -n biopython-%{version}
|
|
find -type f -name "*.py" -exec sed -i '/^#![ ]*\/usr\/bin\/.*$/ d' {} 2>/dev/null ';'
|
|
# Example scripts cannot be in a subdirectory
|
|
mv -v Doc/examples examples
|
|
|
|
%build
|
|
export LANG=en_US.UTF-8
|
|
%python_build
|
|
|
|
%install
|
|
export LANG=en_US.UTF-8
|
|
%python_install
|
|
%python_expand %fdupes %{buildroot}%{$python_sitearch}
|
|
|
|
%if %{with test}
|
|
%check
|
|
export LANG=en_US.UTF-8
|
|
%pytest
|
|
%endif
|
|
|
|
%files %{python_files}
|
|
%doc CONTRIB.rst DEPRECATED.rst NEWS.rst README.rst
|
|
%doc Doc/ examples/
|
|
%license LICENSE.rst
|
|
%{python_sitearch}/Bio/
|
|
%{python_sitearch}/BioSQL/
|
|
%{python_sitearch}/biopython-%{version}-py*.egg-info
|
|
|
|
%changelog
|